The Nucleic Acid Workbench (NAW), a drug deign and chemical simulation program which is specialized to simulate the structure and properties of a wide range of nucleic acid systems, will be developed under this proposal. The software will construct and analyze single, double and triple strand molecules where each strand may be combinations DNA, RNA or PNA (pseudo nucleic acids with modified backbones or linkers) templates in varying conformations. The NAW will be able to simulate properties of these systems using molecular mechanics and molecular dynamics, including energetics of associations and structural variations. A number of commonly used forcefields including CHARMm and CFF95 will be supported, along with an array of charge and solvent models. This comprehensive simulation environment will allow the comparison and testing of the many nucleic acid simulation methodologies which appear in the scientific literature, providing an assessment of the reliability and applicability of computer simulation for these systems. It will be integrated into a modeling environment (Cerius2) which will allow interactions with other specialized modeling software such as protein homology, combinatorial chemistry, and X-ray and nmr workbenches. It will be marketed to research organizations in the pharmaceutical and biotechnology industries, government laboratories and academic institutions. PROPOSED COMMERCIAL APPLICATION: The Nucleic Acid Workbench developed here is a computer simulation program which helps chemists and biochemists understand the structure and properties of DNA and RNA, and is useful in the design of potential drugs and therapies targeted at nucleic acids. It will be marketed to research organization in the pharmaceutical and biotechnology industries, government laboratories and academic institutions.